Snakemake Report

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Workflow

Click the nodes to obtain details about each step.

Read QC

Read Trimming

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

File Code

out_dir:
    '/Users/csifuentes/Documents/outDataModularInclude'
input_dir:
    fastq: '/Users/csifuentes/Documents/testData/simulated_reads/fastq'
    genome_fasta: '/Users/csifuentes/Documents/testData/index/'
    genome_gtf: '/Users/csifuentes/Documents/testData/index/Homo_sapiens.GRCh38.103.gtf'
read_info:
    fastq_suffix: 'fastq'
    r1_suffix: '_1' 
thread_info:
    fastqc: 4
    align: 4
    counts: 4
trim_info:
    tool: 'fastp'
    length: 20
    quality: 30
count_info:
    strand: 0
diffex_info:
    prefix: 'WT_vs_KO'
    metadata: '/Users/csifuentes/Documents/repo/Basic-Bulk-RNA-seq-Workflow/workflow_modularized_include/resources/metadata.txt'

Jobs 12

Input files

/Users/csifuentes/Documents/testData/simulated_reads/fastq/{sample}.fastq.gz

Output files

/Users/csifuentes/Documents/outDataModularInclude/QC/{sample}_fastqc.zip

Conda software stack

fastqc=0.11.9
font-ttf-dejavu-sans-mono=2.37
fontconfig=2.13.1
freetype=2.10.4
icu=58.2
libcxx=10.0.0
libiconv=1.16
libpng=1.6.37
libxml2=2.9.10
openjdk=11.0.6
perl=5.26.2
xz=5.2.5
zlib=1.2.11

Code

1
2
3

        mkdir -p {params.qc_dir}
        fastqc         --noextract         -f {params.format}         -o {params.qc_dir}         -t {threads}         {input.fastq}

Jobs 6

Input files

/Users/csifuentes/Documents/testData/simulated_reads/fastq/{sample}_1.fastq.gz
/Users/csifuentes/Documents/testData/simulated_reads/fastq/{sample}_2.fastq.gz

Output files

/Users/csifuentes/Documents/outDataModularInclude/TRIM/{sample}_val_1.fq
/Users/csifuentes/Documents/outDataModularInclude/TRIM/{sample}_val_2.fq
/Users/csifuentes/Documents/outDataModularInclude/TRIM/{sample}.html
/Users/csifuentes/Documents/outDataModularInclude/TRIM/{sample}.json

Conda software stack

fastp=0.20.1
libcxx=10.0.0
zlib=1.2.11

Code

1 2	`fastp -i {input.r1} -I {input.r2} -o {output.r1} -O {output.r2} -w {threads} -G -h {output.h} -j {output.j} -l {params.length} -q {params.quality}`

Jobs 6

Input files

/Users/csifuentes/Documents/outDataModularInclude/TRIM/{sample}_val_1.fq
/Users/csifuentes/Documents/outDataModularInclude/TRIM/{sample}_val_2.fq

Output files

/Users/csifuentes/Documents/outDataModularInclude/ALIGN/{sample}Aligned.sortedByCoord.out.bam

Conda software stack

star=2.7.8a

Code

1
2

        STAR         --genomeDir {params.index}         --readFilesIn {input.r1} {input.r2}         --sjdbGTFfile {params.gtf}         --outFileNamePrefix {params.out_prefix}         --runThreadN {threads}         --outSAMattributes Standard         --outSAMtype BAM SortedByCoordinate         --outFilterMismatchNmax 999         --alignSJoverhangMin 8         --alignSJDBoverhangMin 1         --outFilterMismatchNoverReadLmax 0.04         --alignIntronMin 20         --alignIntronMax 1000000         --alignMatesGapMax 1000000         --sjdbScore 1

Jobs 1

Input files

/Users/csifuentes/Documents/outDataModularInclude/ALIGN/sample_01Aligned.sortedByCoord.out.bam
/Users/csifuentes/Documents/outDataModularInclude/ALIGN/sample_02Aligned.sortedByCoord.out.bam
/Users/csifuentes/Documents/outDataModularInclude/ALIGN/sample_03Aligned.sortedByCoord.out.bam
/Users/csifuentes/Documents/outDataModularInclude/ALIGN/sample_04Aligned.sortedByCoord.out.bam
/Users/csifuentes/Documents/outDataModularInclude/ALIGN/sample_05Aligned.sortedByCoord.out.bam
/Users/csifuentes/Documents/outDataModularInclude/ALIGN/sample_06Aligned.sortedByCoord.out.bam

Output files

/Users/csifuentes/Documents/outDataModularInclude/COUNTS/counts.txt
/Users/csifuentes/Documents/outDataModularInclude/COUNTS/counts.tmp

Conda software stack

subread=2.0.1
zlib=1.2.11

Code

        featureCounts         -O         -p         -B         -C         -T {threads}         -s {params.strand}         -a {params.gtf}         -o {output.tmp}         {input.bams}

        sed '/^#/d' {output.tmp} | cut -f 1,7- > {output.counts}

Rule properties
Input files
Jobs	1
/Users/csifuentes/Documents/outDataModularInclude/COUNTS/counts.txt
Output files
/Users/csifuentes/Documents/outDataModularInclude/COUNTS/counts_fixed.txt

Jobs 1

Input files

/Users/csifuentes/Documents/outDataModularInclude/COUNTS/counts_fixed.txt

Output files

/Users/csifuentes/Documents/outDataModularInclude/DIFFEX/WT_vs_KO_normCounts.txt
/Users/csifuentes/Documents/outDataModularInclude/DIFFEX/WT_vs_KO_results.txt
/Users/csifuentes/Documents/outDataModularInclude/DIFFEX/WT_vs_KO_sigdiff.txt
/Users/csifuentes/Documents/outDataModularInclude/DIFFEX/WT_vs_KO_vstCounts.txt

Code

1 2	`Rscript {params.script} {params.metadata} {input.counts} {params.out_prefix}`

Jobs 6

Input files

/Users/csifuentes/Documents/outDataModularInclude/ALIGN/{sample}Aligned.sortedByCoord.out.bam

Output files

/Users/csifuentes/Documents/outDataModularInclude/QC/{sample}.pos.DupRate.xls
/Users/csifuentes/Documents/outDataModularInclude/QC/{sample}.seq.DupRate.xls
/Users/csifuentes/Documents/outDataModularInclude/QC/{sample}.DupRate_plot.r
/Users/csifuentes/Documents/outDataModularInclude/QC/{sample}.DupRate_plot.pdf

Conda software stack

_r-mutex=1.0.0
blas=1.0
bwidget=1.9.11
bx-python=0.7.3
bzip2=1.0.8
ca-certificates=2021.4.13
cairo=1.14.12
cctools=927.0.2
certifi=2020.6.20
clang=10.0.0
clang_osx-64=10.0.0
clangxx=10.0.0
clangxx_osx-64=10.0.0
compiler-rt=10.0.0
compiler-rt_osx-64=10.0.0
curl=7.67.0
cython=0.29.14
fontconfig=2.13.1
freetype=2.10.4
fribidi=1.0.10
gettext=0.21.0
gfortran_osx-64=4.8.5
glib=2.63.1
graphite2=1.3.14
gsl=2.4
harfbuzz=2.4.0
icu=58.2
intel-openmp=2021.2.0
jpeg=9b
krb5=1.16.4
ld64=450.3
libcurl=7.67.0
libcxx=10.0.0
libdeflate=1.0
libedit=3.1.20210216
libffi=3.2.1
libgfortran=3.0.1
libiconv=1.16
libllvm10=10.0.1
libpng=1.6.37
libssh2=1.9.0
libtiff=4.1.0
libxml2=2.9.10
llvm-openmp=10.0.0
lz4-c=1.9.3
make=4.2.1
mkl=2019.4
mkl-service=2.3.0
mkl_fft=1.0.15
mkl_random=1.1.0
ncurses=6.2
numpy=1.16.6
numpy-base=1.16.6
openssl=1.1.1k
pango=1.42.4
pcre=8.44
pip=19.3.1
pixman=0.40.0
pysam=0.15.3
python=2.7.18
r-base=3.5.3
readline=8.1
rseqc=2.6.4
setuptools=44.0.0
six=1.15.0
sqlite=3.35.4
tapi=1000.10.8
tk=8.6.10
tktable=2.10
wheel=0.36.2
xz=5.2.5
zlib=1.2.11
zstd=1.4.9

Code

1 2	`read_duplication.py -i {input.bam} -o {params.prefix}`

Jobs 6

Input files

/Users/csifuentes/Documents/outDataModularInclude/ALIGN/{sample}Aligned.sortedByCoord.out.bam

Output files

/Users/csifuentes/Documents/outDataModularInclude/QC/{sample}.GC.xls
/Users/csifuentes/Documents/outDataModularInclude/QC/{sample}.GC_plot.r
/Users/csifuentes/Documents/outDataModularInclude/QC/{sample}.GC_plot.pdf

Conda software stack

_r-mutex=1.0.0
blas=1.0
bwidget=1.9.11
bx-python=0.7.3
bzip2=1.0.8
ca-certificates=2021.4.13
cairo=1.14.12
cctools=927.0.2
certifi=2020.6.20
clang=10.0.0
clang_osx-64=10.0.0
clangxx=10.0.0
clangxx_osx-64=10.0.0
compiler-rt=10.0.0
compiler-rt_osx-64=10.0.0
curl=7.67.0
cython=0.29.14
fontconfig=2.13.1
freetype=2.10.4
fribidi=1.0.10
gettext=0.21.0
gfortran_osx-64=4.8.5
glib=2.63.1
graphite2=1.3.14
gsl=2.4
harfbuzz=2.4.0
icu=58.2
intel-openmp=2021.2.0
jpeg=9b
krb5=1.16.4
ld64=450.3
libcurl=7.67.0
libcxx=10.0.0
libdeflate=1.0
libedit=3.1.20210216
libffi=3.2.1
libgfortran=3.0.1
libiconv=1.16
libllvm10=10.0.1
libpng=1.6.37
libssh2=1.9.0
libtiff=4.1.0
libxml2=2.9.10
llvm-openmp=10.0.0
lz4-c=1.9.3
make=4.2.1
mkl=2019.4
mkl-service=2.3.0
mkl_fft=1.0.15
mkl_random=1.1.0
ncurses=6.2
numpy=1.16.6
numpy-base=1.16.6
openssl=1.1.1k
pango=1.42.4
pcre=8.44
pip=19.3.1
pixman=0.40.0
pysam=0.15.3
python=2.7.18
r-base=3.5.3
readline=8.1
rseqc=2.6.4
setuptools=44.0.0
six=1.15.0
sqlite=3.35.4
tapi=1000.10.8
tk=8.6.10
tktable=2.10
wheel=0.36.2
xz=5.2.5
zlib=1.2.11
zstd=1.4.9

Code

1 2	`read_GC.py -i {input.bam} -o {params.prefix}`